[2023-06-29 19:52:57,181] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:52:57,184] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:52:57,184] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference
[2023-06-29 19:52:58,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:52:58,462] [INFO] Task started: Prodigal
[2023-06-29 19:52:58,462] [INFO] Running command: gunzip -c /var/lib/cwl/stgae016bdc-8ec9-4a57-9b14-c8c49dae0985/GCA_016708085.1_ASM1670808v1_genomic.fna.gz | prodigal -d GCA_016708085.1_ASM1670808v1_genomic.fna/cds.fna -a GCA_016708085.1_ASM1670808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:53:15,341] [INFO] Task succeeded: Prodigal
[2023-06-29 19:53:15,342] [INFO] Task started: HMMsearch
[2023-06-29 19:53:15,342] [INFO] Running command: hmmsearch --tblout GCA_016708085.1_ASM1670808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference/reference_markers.hmm GCA_016708085.1_ASM1670808v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:53:15,606] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:53:15,607] [INFO] Found 6/6 markers.
[2023-06-29 19:53:15,655] [INFO] Query marker FASTA was written to GCA_016708085.1_ASM1670808v1_genomic.fna/markers.fasta
[2023-06-29 19:53:15,656] [INFO] Task started: Blastn
[2023-06-29 19:53:15,656] [INFO] Running command: blastn -query GCA_016708085.1_ASM1670808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference/reference_markers.fasta -out GCA_016708085.1_ASM1670808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:53:16,262] [INFO] Task succeeded: Blastn
[2023-06-29 19:53:16,267] [INFO] Selected 25 target genomes.
[2023-06-29 19:53:16,268] [INFO] Target genome list was writen to GCA_016708085.1_ASM1670808v1_genomic.fna/target_genomes.txt
[2023-06-29 19:53:16,279] [INFO] Task started: fastANI
[2023-06-29 19:53:16,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgae016bdc-8ec9-4a57-9b14-c8c49dae0985/GCA_016708085.1_ASM1670808v1_genomic.fna.gz --refList GCA_016708085.1_ASM1670808v1_genomic.fna/target_genomes.txt --output GCA_016708085.1_ASM1670808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:53:37,519] [INFO] Task succeeded: fastANI
[2023-06-29 19:53:37,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:53:37,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:53:37,539] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:53:37,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:53:37,540] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.4857	113	1180	95	below_threshold
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	76.2805	74	1180	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	76.2639	55	1180	95	below_threshold
Agriterribacter humi	strain=YJ03	GCA_009192765.1	1104781	1104781	type	True	76.2463	64	1180	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.1371	65	1180	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.0959	61	1180	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.0688	55	1180	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	76.0244	68	1180	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	75.9875	58	1180	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.9522	84	1180	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	75.9154	71	1180	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.8954	71	1180	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	75.7819	54	1180	95	below_threshold
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	75.769	53	1180	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.7279	60	1180	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	75.7074	52	1180	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	75.6607	51	1180	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:53:37,542] [INFO] DFAST Taxonomy check result was written to GCA_016708085.1_ASM1670808v1_genomic.fna/tc_result.tsv
[2023-06-29 19:53:37,542] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:53:37,543] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:53:37,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference/checkm_data
[2023-06-29 19:53:37,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:53:37,584] [INFO] Task started: CheckM
[2023-06-29 19:53:37,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708085.1_ASM1670808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708085.1_ASM1670808v1_genomic.fna/checkm_input GCA_016708085.1_ASM1670808v1_genomic.fna/checkm_result
[2023-06-29 19:54:27,585] [INFO] Task succeeded: CheckM
[2023-06-29 19:54:27,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:54:27,610] [INFO] ===== Completeness check finished =====
[2023-06-29 19:54:27,610] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:54:27,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708085.1_ASM1670808v1_genomic.fna/markers.fasta)
[2023-06-29 19:54:27,611] [INFO] Task started: Blastn
[2023-06-29 19:54:27,611] [INFO] Running command: blastn -query GCA_016708085.1_ASM1670808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8f44cd2-6f00-4f44-9a62-d9cff3a769f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708085.1_ASM1670808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:54:28,485] [INFO] Task succeeded: Blastn
[2023-06-29 19:54:28,490] [INFO] Selected 14 target genomes.
[2023-06-29 19:54:28,491] [INFO] Target genome list was writen to GCA_016708085.1_ASM1670808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:54:28,523] [INFO] Task started: fastANI
[2023-06-29 19:54:28,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgae016bdc-8ec9-4a57-9b14-c8c49dae0985/GCA_016708085.1_ASM1670808v1_genomic.fna.gz --refList GCA_016708085.1_ASM1670808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708085.1_ASM1670808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:54:38,514] [INFO] Task succeeded: fastANI
[2023-06-29 19:54:38,529] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:54:38,529] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_016703625.1	s__Ferruginibacter sp016703625	98.1454	1110	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	97.77	96.12	0.94	0.91	5	conclusive
GCA_016710935.1	s__Ferruginibacter sp016710935	79.9938	619	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715365.1	s__Ferruginibacter sp016715365	79.8898	655	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.79	98.54	0.91	0.89	5	-
GCA_016786725.1	s__Ferruginibacter sp016786725	78.9088	545	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710745.1	s__Ferruginibacter sp016710745	78.7697	525	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710165.1	s__Ferruginibacter sp016710165	78.7386	527	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.37	99.37	0.98	0.98	3	-
GCA_016720775.1	s__Ferruginibacter sp016720775	78.4069	516	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983695.1	s__Ferruginibacter sp017983695	77.4774	309	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878475.1	s__Ferruginibacter sp903878475	77.2954	228	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.41	98.13	0.86	0.85	5	-
GCA_018057635.1	s__Ferruginibacter sp018057635	77.2309	140	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721725.1	s__Ferruginibacter sp016721725	76.8686	222	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.24	99.24	0.96	0.96	2	-
GCA_016713965.1	s__Ferruginibacter sp016713965	76.5545	133	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336815.1	s__Ferruginibacter sp002336815	76.4056	121	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	75.8315	87	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:54:38,531] [INFO] GTDB search result was written to GCA_016708085.1_ASM1670808v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:54:38,532] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:54:38,535] [INFO] DFAST_QC result json was written to GCA_016708085.1_ASM1670808v1_genomic.fna/dqc_result.json
[2023-06-29 19:54:38,536] [INFO] DFAST_QC completed!
[2023-06-29 19:54:38,536] [INFO] Total running time: 0h1m41s